Job ID = 1292384 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T09:13:30 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 58,525,121 reads read : 117,050,242 reads written : 58,525,121 reads 0-length : 58,525,121 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:04 58525121 reads; of these: 58525121 (100.00%) were unpaired; of these: 3920676 (6.70%) aligned 0 times 48333107 (82.59%) aligned exactly 1 time 6271338 (10.72%) aligned >1 times 93.30% overall alignment rate Time searching: 00:13:04 Overall time: 00:13:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 49217294 / 54604445 = 0.9013 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 02 Jun 2019 18:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 18:48:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:48:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 18:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 18:48:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:48:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:48:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:48:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:48:33: 1000000 INFO @ Sun, 02 Jun 2019 18:48:34: 1000000 INFO @ Sun, 02 Jun 2019 18:48:36: 1000000 INFO @ Sun, 02 Jun 2019 18:48:41: 2000000 INFO @ Sun, 02 Jun 2019 18:48:43: 2000000 INFO @ Sun, 02 Jun 2019 18:48:47: 2000000 INFO @ Sun, 02 Jun 2019 18:48:49: 3000000 INFO @ Sun, 02 Jun 2019 18:48:51: 3000000 INFO @ Sun, 02 Jun 2019 18:48:56: 4000000 INFO @ Sun, 02 Jun 2019 18:48:58: 3000000 INFO @ Sun, 02 Jun 2019 18:48:59: 4000000 INFO @ Sun, 02 Jun 2019 18:49:03: 5000000 INFO @ Sun, 02 Jun 2019 18:49:06: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:49:06: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:49:06: #1 total tags in treatment: 5387151 INFO @ Sun, 02 Jun 2019 18:49:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:49:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:49:06: #1 tags after filtering in treatment: 5387151 INFO @ Sun, 02 Jun 2019 18:49:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:49:06: #1 finished! INFO @ Sun, 02 Jun 2019 18:49:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:49:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:49:07: #2 number of paired peaks: 2903 INFO @ Sun, 02 Jun 2019 18:49:07: start model_add_line... INFO @ Sun, 02 Jun 2019 18:49:07: start X-correlation... INFO @ Sun, 02 Jun 2019 18:49:07: end of X-cor INFO @ Sun, 02 Jun 2019 18:49:07: #2 finished! INFO @ Sun, 02 Jun 2019 18:49:07: #2 predicted fragment length is 164 bps INFO @ Sun, 02 Jun 2019 18:49:07: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 02 Jun 2019 18:49:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.05_model.r INFO @ Sun, 02 Jun 2019 18:49:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:49:07: 5000000 INFO @ Sun, 02 Jun 2019 18:49:08: 4000000 INFO @ Sun, 02 Jun 2019 18:49:10: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:49:10: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:49:10: #1 total tags in treatment: 5387151 INFO @ Sun, 02 Jun 2019 18:49:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:49:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:49:10: #1 tags after filtering in treatment: 5387151 INFO @ Sun, 02 Jun 2019 18:49:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:49:10: #1 finished! INFO @ Sun, 02 Jun 2019 18:49:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:49:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:49:11: #2 number of paired peaks: 2903 INFO @ Sun, 02 Jun 2019 18:49:11: start model_add_line... INFO @ Sun, 02 Jun 2019 18:49:11: start X-correlation... INFO @ Sun, 02 Jun 2019 18:49:11: end of X-cor INFO @ Sun, 02 Jun 2019 18:49:11: #2 finished! INFO @ Sun, 02 Jun 2019 18:49:11: #2 predicted fragment length is 164 bps INFO @ Sun, 02 Jun 2019 18:49:11: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 02 Jun 2019 18:49:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.10_model.r INFO @ Sun, 02 Jun 2019 18:49:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:49:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:49:19: 5000000 INFO @ Sun, 02 Jun 2019 18:49:22: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:49:22: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:49:22: #1 total tags in treatment: 5387151 INFO @ Sun, 02 Jun 2019 18:49:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:49:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:49:22: #1 tags after filtering in treatment: 5387151 INFO @ Sun, 02 Jun 2019 18:49:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:49:22: #1 finished! INFO @ Sun, 02 Jun 2019 18:49:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:49:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:49:23: #2 number of paired peaks: 2903 INFO @ Sun, 02 Jun 2019 18:49:23: start model_add_line... INFO @ Sun, 02 Jun 2019 18:49:23: start X-correlation... INFO @ Sun, 02 Jun 2019 18:49:23: end of X-cor INFO @ Sun, 02 Jun 2019 18:49:23: #2 finished! INFO @ Sun, 02 Jun 2019 18:49:23: #2 predicted fragment length is 164 bps INFO @ Sun, 02 Jun 2019 18:49:23: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 02 Jun 2019 18:49:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.20_model.r INFO @ Sun, 02 Jun 2019 18:49:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:49:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:49:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:49:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:49:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:49:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:49:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.05_summits.bed INFO @ Sun, 02 Jun 2019 18:49:35: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7890 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:49:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:49:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:49:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.10_summits.bed INFO @ Sun, 02 Jun 2019 18:49:39: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5515 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:49:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:49:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:49:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:49:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3923761/SRX3923761.20_summits.bed INFO @ Sun, 02 Jun 2019 18:49:51: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3326 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。